Question: Selection of terms in clusterProfiler, the inverse of dropGO
0
gravatar for Sebastian Hesse
5 months ago by
Germany / Munich / Dr.von Hauner Children's Hospital
Sebastian Hesse30 wrote:

The clusterProfiler package has the function dropGO to exclude terms from the plotting but is there also a method so select the terms one wants to show?

Im asking because in my cellular component enrichment I have multiple occurrences of eg granule subsets and would specifically choose only non redundant ones (simplify unfortunately can not differentiate here enough to exclude overlaps).

I tried the following:

 excludeCCdown <- down_CC@compareClusterResult$Description
 remove <- c(5, 7, 11, 15, 16, 125) #contains terms I want to keep
 excludeCCdown <- excludeCCdown[! excludeCCdown %in% remove]
 granules_CC_down <- dropGO(down_CC, term = excludeCCdown)

However, the resulting granulesCCdown still contains all the dropped terms.

Thanks for your help! Sebastian

clusterprofiler R • 226 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by Sebastian Hesse30
Answer: Selection of terms in clusterProfiler, the inverse of dropGO
1
gravatar for Sebastian Hesse
5 months ago by
Germany / Munich / Dr.von Hauner Children's Hospital
Sebastian Hesse30 wrote:

Ok, I found a workaround:

excludeCCdown <- data.frame("ID" = down_CC@compareClusterResult$ID, "name" = down_CC@compareClusterResult$Description)
remove <- c("GO:0099503", "GO:0042582", "GO:0042581", "GO:0070820 ", "GO:0101002") #secretory vesicle, azurophil granule, specific granule, tertiary granule, ficolin-1-rich granule
excludeCCdown <- excludeCCdown$ID[! excludeCCdown$ID %in% remove]

granules_CC_down <- dropGO(down_CC, term = excludeCCdown)

So dropGO only uses IDs, not terms. One has to extract all terms with ther IDs into a df and choose from there which IDs to keep aka remove from the list of terms to be dropped. Then all works fine.

ADD COMMENTlink written 5 months ago by Sebastian Hesse30
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